Well, there was stow/xstow...

https://www.gnu.org/software/stow/

https://xstow.sourceforge.net/

Stow only symlinks. That's even one layer below GoboLinux, and GoboLinux is not extremely active either (it is not dead, but kind of semi-dormant, that is sometimes a few changes and improvements are added, then it goes back to hibernation again).